Mercurial > repos > iuc > schicexplorer_schiccorrectmatrices
changeset 1:16dda99bd733 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit 72e1e90ac05a32dbd6fc675073429c0086048b18"
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--- a/macros.xml Wed Jan 29 17:07:16 2020 -0500 +++ b/macros.xml Tue Mar 10 15:14:37 2020 -0400 @@ -1,6 +1,6 @@ <macros> <token name="@THREADS@">\${GALAXY_SLOTS:-4}</token> - <token name="@WRAPPER_VERSION@">1</token> + <token name="@WRAPPER_VERSION@">4</token> <xml name="requirements"> <requirements> @@ -9,8 +9,8 @@ </requirements> <version_command>@BINARY@ --version</version_command> </xml> - <xml name='matrix_mcooler_macro'> - <param name='matrix_mcooler' type="data" format="mcool" + <xml name='matrix_scooler_macro'> + <param name='matrix_scooler' type="data" format="scool" label="Matrix to compute on"/> </xml> <xml name='matrix_cooler_multiple_macro'> @@ -18,7 +18,7 @@ label="Matricies to compute on" multiple="true"/> </xml> <token name="@ESCAPE_IDENTIFIER_FASTQ@"><![CDATA[re.sub('[^\s\w\.]', '_', str($fastq.element_identifier))]]></token> - <token name="@ESCAPE_IDENTIFIER_MCOOL@"><![CDATA[re.sub('[^\s\w\.]', '_', str($matrix_mcooler.element_identifier))]]></token> + <token name="@ESCAPE_IDENTIFIER_SCOOL@"><![CDATA[re.sub('[^\s\w\.]', '_', str($matrix_scooler.element_identifier))]]></token> <token name="@ESCAPE_IDENTIFIER_M@"><![CDATA[re.sub('[^\s\w\-\.]', '_', str($m.element_identifier))]]></token> <xml name="citations">
--- a/scHicCorrectMatrices.xml Wed Jan 29 17:07:16 2020 -0500 +++ b/scHicCorrectMatrices.xml Tue Mar 10 15:14:37 2020 -0400 @@ -7,20 +7,20 @@ <expand macro="requirements" /> <command detect_errors="exit_code"><![CDATA[ @BINARY@ - --matrix '$matrix_mcooler' - --outFileName corrected.mcool + --matrix '$matrix_scooler' + --outFileName corrected.scool --threads @THREADS@ ]]></command> <inputs> - <expand macro="matrix_mcooler_macro"/> + <expand macro="matrix_scooler_macro"/> </inputs> <outputs> - <data name="outFileName" from_work_dir="corrected.mcool" format="mcool" label="${tool.name} on ${on_string}: KR corrected matrix"/> + <data name="outFileName" from_work_dir="corrected.scool" format="scool" label="${tool.name} on ${on_string}: KR corrected matrix"/> </outputs> <tests> <test> - <param name='matrix_mcooler' value='test_matrix.mcool' /> - <output name="outFileName" ftype="mcool"> + <param name='matrix_scooler' value='test_matrix.scool' /> + <output name="outFileName" ftype="scool"> <assert_contents> <has_h5_keys keys='Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/chrom, Diploid_1_CGTACTAG_AAGGAGTA_R1fastqgz/bins/end, @@ -180,7 +180,8 @@ Correct all matrices ==================== -scHicCorrectmatrices is a tool to correct with HiCExplorer's KR algorithm all Hi-C matrices stored in the mcool file. +scHicCorrectmatrices is a tool to correct all Hi-C matrices stored in the provided scool file using HiCExplorer's KR algorithm, which is detailed here: +https://hicexplorer.readthedocs.io/en/latest/content/tools/hicCorrectMatrix.html For more information about scHiCExplorer please consider our documentation on readthedocs.io_
--- a/test-data/scHicQualityControl/qc_report.txt Wed Jan 29 17:07:16 2020 -0500 +++ b/test-data/scHicQualityControl/qc_report.txt Tue Mar 10 15:14:37 2020 -0400 @@ -1,6 +1,6 @@ -# QC report for single-cell Hi-C data generated by scHiCExplorer 1-dev +# QC report for single-cell Hi-C data generated by scHiCExplorer 4 scHi-C sample contained 20 cells: Number of removed matrices containing bad chromosomes 0 -Number of removed matrices due to low read coverage (< 100000): 8 +Number of removed matrices due to low read coverage (< 100000): 10 Number of removed matrices due to too many zero bins (< 0.001 density, within 30000000 relative genomic distance): 0 -12 samples passed the quality control. Please consider matrices with a low read coverage may be the matrices with a low density and overlap therefore. \ No newline at end of file +10 samples passed the quality control. Please consider matrices with a low read coverage may be the matrices with a low density and overlap therefore. \ No newline at end of file